rs975404

Variant names:

• chr4-122600137-T-C
• rs975404
• ENST00000776599.1:n.556+2269A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000776599.1(ENSG00000301148):​n.556+2269A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 151,690 control chromosomes in the GnomAD database, including 8,696 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.33 (8696 hom., cov: 30)
• Consequence: ENSG00000301148 ENST00000776599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 3 publications found

Genes affected

ENSG00000301148 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301148	ENST00000776599.1	n.556+2269A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50250 AN: 151572 Hom.: 8685 Cov.: 30

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.331

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.332 AC: 50286 AN: 151690 Hom.: 8696 Cov.: 30 AF XY: 0.321 AC XY: 23754 AN XY: 74100

African (AFR) AF: 0.385 AC: 15886 AN: 41316

American (AMR) AF: 0.257 AC: 3911 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1295 AN: 3464

East Asian (EAS) AF: 0.134 AC: 688 AN: 5128

South Asian (SAS) AF: 0.210 AC: 1011 AN: 4808

European-Finnish (FIN) AF: 0.237 AC: 2495 AN: 10528

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23846 AN: 67910

Other (OTH) AF: 0.327 AC: 688 AN: 2104

Alfa AF: 0.337 Hom.: 5237

Bravo AF: 0.337

Asia WGS AF: 0.202 AC: 705 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.85
PhyloP100		-1.8

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs975404; hg19: chr4-123521292;